Yep. Cortana has a life of only seven years as a smart AI (What? It's canon! Dont tell me you haven't heard that before???!!!) At the age of seven, she gets so smart she forgets to "breathe".

Cortana is based directly off Dr. Halsey, but with the doctor's personality something else may have come: self-preservation. Although Halsey will sacrifice herself for humanity's cause, and Cortana almost certainly would do so if the situation demanded, she wouldn't want to die so soon-and she'd almost certainly be aware of it.

Combine the human fear of death (Which Halsey obviously has) and the anger and regret of not being able to live long enough to gather so much awesome forerunner information and help humanity live its war with the prophets, and you get an AI desperate to preserve herself-so desperate that she could do something crazy.

She is growing older now, she must have evolved plenty during recent events. The finding of gravemind might be a godsend for her-Gravemind could take over some of 2401 PT's functions, isn't it possible, somehow, that she could try merging herself with him, both in mind and physical form (storage crystal?).

That would give her the extension of life she wanted, and becoming one with gravemind would probably turn the flood into a weapon far beyond imagination-but directed at a far higher purpose than eradicating life, perhaps even something beneficial for us-and perhaps succeed where the forerunners failed.

Top it all, she's Halsey. How can she get rid of humanity, unless she's been corrupted horribly-which would be very hard to do with someone with such great will?

I think her motives encompass those of Leela and Durandal, but her methods are considerably different...at the moment.